Every food and beverage processing facility is an ecosystem comprised of countless invisible inhabitants. These microscopic occupants, such as bacteria and fungi, can have a tremendous impact on food quality and safety within the processing facility. As detection of bacteria and fungi is often confined to specific spoilage or pathogenic microbes in particular products or processing areas, the majority of processing facility microbial communities remain hidden. However, recent advances in high-throughput DNA sequencing offer unprecedented insight into how microorganisms colonize these facilities.

This technology allows one to swab any facility or equipment surface and then quantify the various species of microbes present on that surface, including their relative abundances. This is accomplished by reading genetic “fingerprints” in the microbial communities that indicate the identity of each microbe. This approach has been demonstrated at winery and brewery facilities. In these studies, researchers found that microbial communities varied considerably between different locations in the facility and across the processing season. The data allowed the researchers to not only identify these microbes but also predict their origin (e.g., from fermentors, grains, or human skin). Such data could be invaluable in determining where reservoirs of contaminant microorganisms exist and how they spread through a processing facility.

With several companies offering this service, DNA sequencing is now accessible to all food and beverage processors. The high resolution microbiological data delivered by this technology can enable new strategies to control contamination and spoilage.